Fig. 2.

Preprocessing of experimental spectrum pairs for experiments with labeled linkers. DSS D₀/D₁₂ is used as an example. Two experimental spectra from the same peptide pair but a different linker mass are matched without a mass shift and with a mass shift of the label mass difference considering multiple charges. The result is a linear ion spectrum with unknown charges and a cross-linked ion spectrum with known ion charges. This allows for a more constrained and targeted matching to theoretical peaks.